What software to use as an all-around solution for mining GIS?

Target for ArcGIS was pretty good when I used it a couple of years ago - it may be even better now. At that point it didn't really integrate closely enough with ArcGIS to fill the gap for us. There is lots of software that let you work with data in cross section view but few built on top of ArcGIS. I haven't used either of these but you could take a look at Lynx Seismap or CrossView. There is also Xacto X-Section which is free.

When it comes to 3D, Discover 3D has one of the best, most flexible, 3D engines I've used but also has a 'cutting plane' section that lets you move through your data in section view. I think a section view, as well as a full 3D perspective view, is critical as it eliminates the difficulties in editing with a perspective view. It also gives you a much better view of the subsurface at any point - whereas many 3D viewers leave you looking at only the shallowest or 'closest' parts of your model. Discover 3D also has a good selection of 3D feature editing tools and import and export options pretty well aligned with software used in the minerals sector. It supports shapefile and ermapper grid - so it is possible to work with it in conjunction with ArcGIS. It's owned by Pitney Bowes though, who also own Mapinfo, so that integration is unlikely to get better unless the FBGD API lets them add that as a supported format.

Not ArcGIS plugins but you could also look at GoCad - which is extremely powerful but also expensive. Geomodeller is worth a look too.

Personally I'm not convinced that editing models is best done in the 3D view itself. Instead my approach has been to try and smooth transfer, or automatically 'sync' data between different tools so that, for example, input data can be created and edited in both plan view (with ArcMap) and in section view - which pretty well mimics a traditional geological workflow. You might do the same but with data created in a non-ArcGIS environment such as seismic workstations. There's lots of options for actually building the 3D features from that input data, whether that is as dxd or multipatch or whatever, through geoprocessing tools or extensions.